A critical hydrological process is the interaction between rivers and aquifers. However, accurately determining this interaction from one method alone is difficult. At a point, the water exchange in the riverbed can be determined using temperature variations over depth. Over the river reach, differential gauging can be used to determine averaged losses or gains. This study combines these two methods and applies them to a 34 km reach of a semiarid river in eastern Australia under highly transient conditions. It is found that high and low river flows translate into high and low riverbed Darcy fluxes, and that these are strongly losing during high flows, and only slightly losing or gaining for low flows. The spatial variability in riverbed Darcy fluxes may be explained by riverbed heterogeneity, with higher variability at greater spatial scales. Although the river-aquifer gradient is the main driver of riverbed Darcy flux at high flows, considerable uncertainty in both the flux magnitude and direction estimates were found during low flows. The reach-scale results demonstrate that high-flow events account for 64% of the reach loss (or 43% if overbank events are excluded) despite occurring only 11% of the time. By examining the relationship between total flow volume, river stage and duration for in-channel flows, we find the loss ratio (flow loss/total flow) can be greater for smaller flows than larger flows with similar duration. Implications of the study for the modeling and management of connected water resources are also discussed.